Reproduction is a fundamental aspect of life that affects all levels of biology, from genomes and development to population dynamics and diversification. The first Tree of Sex database synthesized a vast diversity of reproductive strategies and their intriguing distribution throughout eukaryotes. A decade on, we are reviving this initiative and greatly expanding its scope to provide the most comprehensive integration of knowledge on eukaryotic reproduction to date. In this perspective, we first identify important gaps in our current knowledge of reproductive strategies across eukaryotes. We then highlight a selection of questions that will benefit most from this new Tree of Sex project, including those related to the evolution of sex, modes of sex determination, sex chromosomes, and the consequences of various reproductive strategies. Finally, we outline our vision for the new Tree of Sex database and the consortium that will create it (treeofsex.org). The new database will cover all Eukaryota and include a wide selection of biological traits. It will also incorporate genomic data types that were scarce or non-existent at the time of the first Tree of Sex initiative. The new database will be publicly accessible, stable, and self-sustaining, thus greatly improving the accessibility of reproductive knowledge to researchers across disciplines for years to come. Lastly, the consortium will persist after the database is created to serve as a collaborative framework for research, prioritizing ethical standards in the collection, use, and sharing of reproductive data. The new Tree of Sex consortium is open, and we encourage all who are interested in this topic to join us.

• Klíčová slova
• asexual reproduction, biodiversity, database, ontology, sex chromosomes, sex determination, sexual reproduction,
• MeSH
• biologická evoluce * MeSH
• Eukaryota * fyziologie   genetika   MeSH
• procesy určující pohlaví MeSH
• rozmnožování * genetika   MeSH
• Publikační typ
• časopisecké články MeSH

For a long time, snakes were presented as a textbook example of a group with gradual differentiation of homologous ZZ/ZW sex chromosomes. However, recent advances revealed that the ZZ/ZW sex chromosomes characterize only caenophidian snakes and certain species of boas and pythons have nonhomologous XX/XY sex chromosomes. We used genome coverage analysis in four non-caenophidian species to identify their sex chromosomes, and we examined the homology of sex chromosomes across phylogenetically informative snake lineages. We identified sex chromosomes for the first time in 13 species of non-caenophidian snakes, providing much deeper insights into the evolutionary history of snake sex chromosomes. The evolution of sex chromosomes in snakes is more complex than previously thought. Snakes may have had ancestral XX/XY sex chromosomes, which are still present in a blind snake and some boas, and there were several transitions to derived XX/XY sex chromosomes with different gene content and two or even three transitions to ZZ/ZW sex chromosomes. However, we discuss more alternative scenarios. In any case, we document that (1) some genomic regions were likely repeatedly co-opted as sex chromosomes in phylogenetically distant lineages, even with opposite types of heterogamety; (2) snake lineages differ greatly in the rate of differentiation of sex chromosomes; (3) snakes likely originally possessed sex chromosomes prone to turnovers. The sex chromosomes became evolutionarily highly stable once their differentiation progressed in the megadiverse caenophidian snakes. Snakes thus provide an ideal system for studying the evolutionary factors that drive unequal rates of differentiation, turnovers and stability of sex chromosomes.

• Klíčová slova
• DNA-seq, genomics, qPCR, reptiles, sex chromosomes, sex determination,
• MeSH
• biologická evoluce MeSH
• fylogeneze MeSH
• hadi * genetika   MeSH
• molekulární evoluce MeSH
• pohlavní chromozomy * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Sex chromosomes of some closely related species are not homologous, and sex chromosome turnover is often attributed to mechanisms that involve linkage to or recombination arrest around sex-determining loci. We examined sex chromosome turnover and recombination landscapes in African clawed frogs (genus Xenopus) with reduced representation genome sequences from 929 individuals from 19 species. We recovered extensive variation in sex chromosomes, including at least eight nonhomologous sex-associated regions-five newly reported here, with most maintaining female heterogamety, but two independent origins of Y chromosomes. Seven of these regions are found in allopolyploid species in the subgenus Xenopus, and all of these reside in one of their two subgenomes, which highlights functional asymmetry between subgenomes. In three species with chromosome-scale genome assemblies (Xenopus borealis, Xenopus laevis, and Xenopus tropicalis), sex-specific recombination landscapes have similar patterns of sex differences in rates and locations of recombination. Across these Xenopus species, sex-associated regions are significantly nearer chromosome ends than expected by chance, even though this is where the ancestral recombination rate is highest in both sexes before the regions became sex associated. As well, expansions of sex-associated recombination arrest occurred multiple times. New information on sex linkage along with among-species variation in female specificity of the sex-determining gene dm-w argues against a "jumping gene" model, where dm-w moves around the genome. The diversity of sex chromosomes in Xenopus raises questions about the roles of natural and sexual selection, polyploidy, the recombination landscape, and neutral processes in driving sex chromosome turnover in animal groups with mostly heterogametic females.

• Klíčová slova
• allopolyploidization, genetic linkage, recombination landscape, sex chromosome turnover, sex determination,
• MeSH
• pohlavní chromozomy * genetika   MeSH
• procesy určující pohlaví MeSH
• rekombinace genetická MeSH
• Xenopus * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Sex chromosome replacement is frequent in many vertebrate clades, including fish, frogs, and lizards. In order to understand the mechanisms responsible for sex chromosome turnover and the early stages of sex chromosome divergence, it is necessary to study lineages with recently evolved sex chromosomes. Here we examine sex chromosome evolution in a group of African cichlid fishes (tribe Tropheini) which began to diverge from one another less than 4 MYA. We have evidence for a previously unknown sex chromosome system, and preliminary indications of several additional systems not previously reported in this group. We find a high frequency of sex chromosome turnover and estimate a minimum of 14 turnovers in this tribe. We date the origin of the most common sex determining system in this tribe (XY-LG5/19) near the base of one of two major sub-clades of this tribe, about 3.4 MY ago. Finally, we observe variation in the size of one sex-determining region that suggests independent evolution of evolutionary strata in species with a shared sex-determination system. Our results illuminate the rapid rate of sex chromosome turnover in the tribe Tropheini and set the stage for further studies of the dynamics of sex chromosome evolution in this group.

• MeSH
• cichlidy * genetika   MeSH
• fylogeneze MeSH
• jezera MeSH
• mitochondriální DNA genetika   MeSH
• molekulární evoluce MeSH
• pohlavní chromozomy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Tanzanie MeSH
• Názvy látek
• mitochondriální DNA MeSH

Geckos are an excellent group to study the evolution of sex determination, as they possess a remarkable variability ranging from a complete absence of sex chromosomes to highly differentiated sex chromosomes. We explored sex determination in the Madagascar leaf-tail geckos of the genus Uroplatus. The cytogenetic analyses revealed highly heterochromatic W chromosomes in all three examined species (Uroplatus henkeli, U. alluaudi, U. sikorae). The comparative gene coverage analysis between sexes in U. henkeli uncovered an extensive Z-specific region, with a gene content shared with the chicken chromosomes 8, 20, 26 and 28. The genomic region homologous to chicken chromosome 28 has been independently co-opted for the role of sex chromosomes in several vertebrate lineages, including monitors, beaded lizards and monotremes, perhaps because it contains the amh gene, whose homologs were repeatedly recruited as a sex-determining locus. We demonstrate that all tested species of leaf-tail geckos share homologous sex chromosomes despite the differences in shape and size of their W chromosomes, which are not homologous to the sex chromosomes of other closely related genera. The rather old (at least 40 million years), highly differentiated sex chromosomes of Uroplatus geckos can serve as a great system to study the convergence of sex chromosomes evolved from the same genomic region.

• Klíčová slova
• DNA-seq, cytogenetics, evolution, genomics, qPCR, reptiles, sex chromosomes, sex determination,
• MeSH
• fylogeneze MeSH
• ještěři * genetika   MeSH
• pohlavní chromozomy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Madagaskar MeSH

Amphibians have highly diverse sex-determining modes leading to a notable interest in vertebrate sex determination and sex chromosome evolution. The identification of sex-determining systems in amphibians, however, is often difficult as a vast majority consist of homomorphic sex chromosomes making them hard to distinguish. In this study, we used Diversity Array Technology sequencing (DArTseq) to identify the sex-determining system in the ornate burrowing frog from Australia, Platyplectrum ornatum. We applied DArTseq to 44 individuals, 19 males and 25 females, collected from two locations to develop sex-linked markers. Unexpectedly, these 44 individuals were classified into two distinct population clusters based on our SNP analyses, 36 individuals in cluster 1, and 8 individuals in cluster 2. We then performed sex-linkage analyses separately in each cluster. We identified 35 sex-linked markers from cluster 1, which were all associated with maleness. Therefore, P. ornatum cluster 1 is utilising a male heterogametic (XX/XY) sex-determining system. On the other hand, we identified 210 sex-linked markers from cluster 2, of which 89 were male specific, i.e., identifying XX/XY sex determining system and 111 were female specific, i.e., identifying ZZ/ZW sex determining system, suggesting existence of either male or female heterogametic sex determining system in cluster 2. We also performed cytogenetic analyses in 1 male and 1 female from cluster 1; however, we did not detect any visible differentiation between the X and Y sex chromosomes. We also mapped sex-linked markers from the two clusters against the P. ornatum genome and our comparative analysis indicated that the sex chromosomes in both clusters shared homologies to chromosome 10 (autosome) of Rana temporaria and ZWY sex chromosome of Xenopus tropicalis. Our preliminary data suggest that it is plausible that the cluster 2 has a potential to be either male or female heterogamety in sex determination, requiring further investigation.

• MeSH
• biologické markery MeSH
• lidé MeSH
• pohlavní chromozomy * genetika   MeSH
• Rana temporaria MeSH
• Xenopus MeSH
• žáby * genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Austrálie MeSH
• Názvy látek
• biologické markery MeSH

Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7-10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

• Klíčová slova
• anurans, genome assembly, hybrid zone, large-scale synteny, linkage map, population pileups diplotyping, segregation distortion, sex-determining region, targeted capture,
• MeSH
• genetická vazba MeSH
• genom * MeSH
• larva MeSH
• mapování chromozomů MeSH
• žáby * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

• Klíčová slova
• evolution, sex chromosomes, sex determination, vertebrates,
• MeSH
• biologická evoluce * MeSH
• obratlovci genetika   růst a vývoj   MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

• Klíčová slova
• amniotes, co-option, sex chromosomes, vertebrates,
• MeSH
• biologická evoluce * MeSH
• plazi genetika   růst a vývoj   MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * MeSH
• ptáci genetika   růst a vývoj   MeSH
• savci genetika   růst a vývoj   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

• Klíčová slova
• clonal reproduction, evolution, hybridization, sex chromosomes, speciation,
• MeSH
• hybridizace genetická * MeSH
• meióza * MeSH
• obratlovci genetika   MeSH
• pohlavní chromozomy genetika   MeSH
• polyploidie * MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH